No, Jennifer Garner was not pregnant on the set of Valentine's Day.
Jennifer gave birth to her 2nd child at age 36, a daughter Seraphina Rose Elizabeth Affleck on January 6, 2009. She returned to work after 6 months to begin filming Valentine's Day (2010).
What we found is that she was 3 months pregnant with her son Samuel Garner Affleck when she completed filming on The Odd Life of Timothy Green (2012).
In latest buzz, nearly two years after they first announced their split (June 2015), Jennifer Garner is gearing up to file for divorce from Ben Affleck. Find out more at Us Weekly.